Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera

Abstract

Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges.

Viral Diversity in Samples of Freshwater Gastropods Benedictia baicalensis (Caenogastropoda: Benedictiidae) Revealed by Total RNA-Sequencing

“…Newly identified viruses from Baikal mollusks have expanded the unique diversity of viruses previously discovered in the waters of Lake Baikal [86,87] and in the endemic Baikal sponges [69,72]. The viral diversity in Baikal endemic gastropods B. baicalensis included the unknown representatives of different orders and families and of two main phyloge-netic branches [37].…”

“…All Baikal mollusk metatranscriptomic data (Table 1) were aggregated into one array for de novo cross-assembly as recommended in other viral community studies [72]. For cross-assembly, the MEGAHIT v.1.2.9 NGS assembler optimized for metagenomics was used with default options [34].…”

Viromes of Coastal Waters of the North Caspian Sea: Initial Assessment of Diversity and Functional Potential

“…Reads related to virophages predominated in the MSC sample, as did those related to mimiviruses. Other studies of viromes [46,[74][75][76] showed that virophages are widely spread throughout the world in a variety of environments, both marine and freshwater. In addition to virophages and tailed phages, viruses of seven other different families were quantitatively predominant in the MSC compared to the SUR and SBI samples.…”

“…All the genomic data (Table 1) were aggregated into one array for de novo crossassembly as recommended [46]. For cross-assembly, the MEGAHIT assembler was used with default options [49].…”

Performance Analysis of Cross-Assembly of Metatranscriptomic Datasets in Viral Community Studies

“…Существует другой подход, при котором после фильтрации по качеству наборов данных из нескольких образцов все прочтения объединяются в один массив и производится единая de novo сборка («cross-assembly»). В наших предыдущих метавиромных исследованиях мы использовали этот подход для сравнения вирусного разнообразия нескольких образцов [16][17][18]. В полученной геномной сборке (далее микс-сборке) скаффолды тестируются одним из алгоритмов на основе HMM метода для поиска потенциальных фрагментов вирусных геномов (фрагментов геномов РНКсодержащих вирусов и транскрибируемых генов ДНК-содержащих вирусов в случае метатранскриптомов).…”